miRNA: 3'- -UCuu-UGG-GUCGUCAGUAUuCUG-GUga -5'
miRNA: 3'- uCUUUg--------GGUCGUCAGUauUCUGGUGa -5'
miRNA: 3'- -UCUU----UGGGUCGU---CAGUAUUCUGGUGa -5'
miRNA: 3'- ucuUUGGGUCGUCAGuAUuCUGGUGA- -5'
miRNA: 3'- -UCUUUGGGUCGUCAGUAUUCUGGUGA- -5'
Results 1 - 5 of 5 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. | strand | Start Position | R_P_ratio# |
P value
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| Predicted miRNA align pattern | |||||||
| 33001 | 3' | -49.5 | NC_007456.1 | + | 16727 | 0.66 | 0.892375 |
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Target: 5'- uAGucuGCCuCAGCAGUCGUAuGACuCAg- -3' miRNA: 3'- -UCuu-UGG-GUCGUCAGUAUuCUG-GUga -5' |
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| 33001 | 3' | -49.5 | NC_007456.1 | + | 21469 | 0.67 | 0.831048 |
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Target: 5'- cGAAAaucaucacaUCGGCAGUCAgcAGACCAUc -3' miRNA: 3'- uCUUUg--------GGUCGUCAGUauUCUGGUGa -5' |
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| 33001 | 3' | -49.5 | NC_007456.1 | + | 10337 | 0.68 | 0.790429 |
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Target: 5'- aAGAGggucGCCCGGUAaauGUCGUAGGGUCACa -3' miRNA: 3'- -UCUU----UGGGUCGU---CAGUAUUCUGGUGa -5' |
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| 33001 | 3' | -49.5 | NC_007456.1 | + | 7120 | 0.68 | 0.779761 |
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Target: 5'- --cAACCCAGUGGUCuUAuGACUGCUg -3' miRNA: 3'- ucuUUGGGUCGUCAGuAUuCUGGUGA- -5' |
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| 33001 | 3' | -49.5 | NC_007456.1 | + | 7191 | 1.09 | 0.002222 |
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Target: 5'- aAGAAACCCAGCAGUCAUAAGACCACUg -3' miRNA: 3'- -UCUUUGGGUCGUCAGUAUUCUGGUGA- -5' |
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Note:
When operating RNAhybrid, the pipeline first calculates the perfect minimum free energy (Perfect mfe *) of a putative miRNA when the entire putative miRNA binds to a perfectly complementary target site, then it calculates the minimum free energy of RNA duplex (mfe of the miRNA/mRNA duplex), abbreviated as Rd_mfe. An alignment for which the Rd_mfe to its correspondent Perfect mfe ratio (R_P_ratio #) is more than 66% is regarded as a positive alignment as described by Krek et al. (21). The P_value is calculated by RNAhybrid.
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